// $Id: nrnoc.hoc,v 1.26 2000/11/27 22:00:19 billl Exp $
proc nrnoc () {}
// Users should not edit nrnoc.hoc or default.hoc. Any local
// changes to these files should be made in local.hoc.
// key '*&*' is picked up by to indicate command for emacs
proc elisp () { printf("*&* %s\n",$s1) }
// if (not exists(simname)) { strdef simname, output_file, datestr, comment }
// Simctrl.hoc will automatically load stdgraph.hoc which automatically
// loads stdrun.hoc
strdef temp_string_, user_string_ // needed for simctrl
/* Global variable default values. NOTE that stdrun.hoc, stdgraph.hoc
and simctrl.hoc all contain variable definitions and thus default.hoc
should be loaded after these files */
load_file("default.hoc") /* Load default.hoc */
/* Allows arrays of strings */
objref hoc_obj_[2]
if (xwindows) {
load_file("stdgui.hoc") // don't want to encounter other String tempate defs
load_file("simctrl.hoc")
} else {
load_file("stdlib.hoc")
load_file("stdrunnoiv.hoc")
}
proc run () {
stdinit()
if (batch_flag == 1) {
sprint(output_file,"data/b%s.%02d", datestr, runnum)
batch_run(tstop, printStep, output_file)
finish()
} else {
continueRun(tstop)
}
}
proc continueRun() { local eventCount
// Although this works properly "the first time" it may not properly "continue" a simulation
eventCount=0
eventslow=1
stoprun = 0
while (t < $1 && stoprun == 0) {
for i = 1, nstep_steprun { fadvance() }
outputData()
eventCount = eventCount + 1
if (xwindows && eventCount%eventStep < 0.1) { doEvents() }
}
finish()
}
proc stdinit() {
realtime=0 startsw()
t = 0
stoprun = 0
if (batch_flag == 1) {
batch_save()
batchSave() // User defined program to set up stuff to save
}
init()
init()
if (graph_flag == 1) {
if (iv_flag == 1) {
initPlot()
} else {
initGraph()
}
}
if (print_flag == 1) { initPrint() }
}
proc init () {
initMech()
initMisc1()
/* Initialize state vars then calculate currents */
/* If user hand-set v in initMisc1() then v_init should be > 1000,
else all compartments will be set to v_init */
if (v_init < 1000) {
finitialize(v_init)
} else {
finitialize()
}
fcurrent()
/* Set ca pump and leak channel for steady state */
setMemb()
/* Recalculate currents with new pump and leak kinetics */
fcurrent()
fcurrent()
initMisc2()
if (cvode_active()) cvode.re_init()
}
proc initMech() { /* Initialization of mechanism variables */
/* NOTE: if any changes are made to the NEURON block of any local mod
file, the user must add the necessary inits to initMisc1() */
/** Range variables **/
forall {
if ((!ismembrane("pas")) && (!ismembrane("Passive"))) {
// Allow for either pas or Passive mod file usage
errorMsg("passive not inserted")
}
if (ismembrane("na_ion")) {
nai = na_init
nai0_na_ion = na_init
}
if (ismembrane("k_ion")) {
ki = k_init
ki0_k_ion = k_init
}
if (ismembrane("ca_ion")) {
cai = ca_init
cai0_ca_ion = ca_init
}
}
/** Global variables **/
}
proc setMemb () { local i_forward, i_back, iSum
/* Setup steady state voltage using leak channel */
forall {
if (ismembrane("pas")) {
iSum = 0.0
if (ismembrane("na_ion")) { iSum = iSum + ina }
if (ismembrane("k_ion")) { iSum = iSum + ik }
if (ismembrane("ca_ion")) { iSum = iSum + ica }
if (ismembrane("ns_ion")) { iSum = iSum + ins } // Non-specific
if (iSum == 0) { // Pas cmp so set e_pas = v
e_pas = v
} else {
if (g_pas > 0) { // Assume g set by user, calc e
e_pas = v + iSum/g_pas
} else { // Assume e set by user, calc g
if (e_pas != v) {
g_pas = iSum/(e_pas - v)
} else { // error: g_pas <= 0
errorMsg("bad g", g_pas)
}
}
if (e_pas < -100 || e_pas > 0) {
errorMsg("erev out of bounds", e_pas)
}
}
} else if (ismembrane("Passive")) {
iSum = 0.0
if (ismembrane("na_ion")) { iSum = iSum + ina }
if (ismembrane("k_ion")) { iSum = iSum + ik }
if (ismembrane("ca_ion")) { iSum = iSum + ica }
if (ismembrane("ns_ion")) { iSum = iSum + ins } // Non-specific
if (iSum == 0) { // Passive cmp so set erev_Passive = v
erev_Passive = v
} else {
if (g_Passive > 0) { // Assume g set by user, calc erev
erev_Passive = v + iSum/g_Passive
} else { // Assume erev set by user, calc g
if (erev_Passive != v) {
g_Passive = iSum/(erev_Passive - v)
} else { // error: g_Passive <= 0
errorMsg("bad g", g_Passive)
}
}
if (erev_Passive < -100 || erev_Passive > 0) {
errorMsg("erev out of bounds", erev_Passive)
}
}
}
}
}
proc finish() {
/* Called following completion of continueRun() */
finishMisc()
if (graph_flag == 1) {
if (iv_flag == 1) {
flushPlot()
} else {
graphmode(-1)
plt(-1)
}
}
if (print_flag == 1) {
wopen("")
}
}
/*------------------------------------------------------------
User definable GRAPHICS and PRINTING routines
------------------------------------------------------------*/
proc outputData() {
// Default procedure - if outputData() doesn't exist in the run file
if (graph_flag == 1) {
if (iv_flag == 1) {
Plot()
rt = stopsw()
if (rt > realtime) {
realtime = rt
fastflushPlot()
doNotify()
if (realtime == 2 && eventcount > 50) {
eventslow = int(eventcount/50) + 1
}
eventcount = 0
}else{
eventcount = eventcount + 1
if ((eventcount%eventslow) == 0) {
doEvents()
}
}
} else {
graph(t)
}
}
if (print_flag == 1) {
if (t%printStep <= printStep) { printOut() }
}
}
proc printOut() {
/* Default procedure - if printOut() doesn't exist in the run file */
}
proc initGraph() {
/* Default procedure - if initGraph() doesn't exist in the run file */
graph()
}
proc initPrint() {
/* Default procedure - if initPrint() doesn't exist in the run file */
wopen(output_file)
}
/*------------------------------------------------------------
User definable BATCH RUN routines
------------------------------------------------------------*/
proc batchSave() {
/* Default procedure - if batchSave() doesn't exist in the run file */
}
proc nextrun() {
// Called from finishmisc() following completion of batch in an autorun
wopen("")
runnum = runnum + 1
sprint(output_file,"data/b%s.%02d", datestr, runnum)
}
// commands for emacs
proc update_runnum() {
runnum = $1
sprint(output_file,"data/%s.%02d", datestr, runnum)
print "^&^ (progn (sim-index-revert)(setq sim-runnum ",runnum,"))" }
proc nrn_write_index() { printf("&INDEX& %s\n",$s1) }
proc nrn_update () { elisp("nrn-update") }
proc nrn_message () { printf("!&! %s\n",$s1) }
/*------------------------------------------------------------
User definable INITIALIZATION and FINISH routines
------------------------------------------------------------*/
// Default procedure - if initMisc1() doesn't exist in the run file
// Initializations performed prior to finitialize()
// This should contain point process inits and inits for any changes
// made to the NEURON block of any local mod file
proc initMisc1() { }
// Default procedure - if initMisc2() doesn't exist in the run file
// Initializations performed after finitialize()
proc initMisc2() { }
// Default procedure - if finishMisc() doesn't exist in the run file
proc finishMisc() { }
/*------------------------------------------------------------
Miscellaneous routines
------------------------------------------------------------*/
proc errorMsg() {
/* Print warning, assumes arg1 is string and arg2 if present is a
variable value */
sectionname(section)
if (numarg() == 0) {
printf("ERROR in errorMsg(): Needs at least 1 argument.\n")
} else if (numarg() == 1) {
printf("ERROR: %s in section %s.\n", $s1, section)
} else {
printf("ERROR: %s in section %s (var=%g).\n", $s1, section, $2)
}
}
proc clear() {
/* Clear non-interviews plot window */
plt(-3)
}
func mod() { local x, y
/* Mod function for non-integers */
x=$1
y=$2
return (x/y - int(x/y))
}
proc whatSection() {
/* Print name of section */
sectionname(section)
print section
}
proc print_pp_location() { local x //arg1 must be a point process
x = $o1.get_loc()
sectionname(temp_string_)
printf("%s located at %s(%g)\n", $o1, temp_string_, x)
pop_section()
}
//* Load local modifications to nrnoc.hoc and default.hoc
load_file("local.hoc")
if (xwindows && graph_flag) { nrnmainmenu() } // pwman_place(50,50)
print "Init complete.\n"
